nstd64 (Wang et al. 2007)
- Organism:
- Human
- Study Type:
- Control Set
- Submitter:
- Database of Genomic Variants
- Description:
- Comprehensive identification and cataloging of copy number variations (CNVs) is required to provide a complete view of human genetic variation. The resolution of CNV detection in previous experimental designs has been limited to tens or hundreds of kilobases. Here we present PennCNV, a hidden Markov model (HMM) based approach, for kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data. This algorithm incorporates multiple sources of information, including total signal intensity and allelic intensity ratio at each SNP marker, the distance between neighboring SNPs, the allele frequency of SNPs, and the pedigree information where available. We applied PennCNV to genotyping data generated for 112 HapMap individuals; on average, we detected approximately 27 CNVs for each individual with a median size of approximately 12 kb. Excluding common rearrangements in lymphoblastoid cell lines, the fraction of CNVs in offspring not detected in parents (CNV-NDPs) was 3.3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping. See Variant Summary counts for nstd64 in dbVar Variant Summary.
- Publication(s):
- Wang et al. 2007
Detailed Information: Download 1383 Variant Regions, Download 2987 Variant Calls, Download Both, FTP
Variant Summary
Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI35 (hg17)
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.11 | Chr1 | 90 | 218 | Remapped | NC_000001.11 |
| NC_000002.12 | Chr2 | 117 | 275 | Remapped | NC_000002.12 |
| NC_000003.12 | Chr3 | 77 | 175 | Remapped | NC_000003.12 |
| NC_000004.12 | Chr4 | 91 | 221 | Remapped | NC_000004.12 |
| NC_000005.10 | Chr5 | 80 | 172 | Remapped | NC_000005.10 |
| NC_000006.12 | Chr6 | 68 | 159 | Remapped | NC_000006.12 |
| NC_000007.14 | Chr7 | 90 | 159 | Remapped | NC_000007.14 |
| NC_000008.11 | Chr8 | 85 | 215 | Remapped | NC_000008.11 |
| NC_000009.12 | Chr9 | 66 | 90 | Remapped | NC_000009.12 |
| NC_000010.11 | Chr10 | 48 | 124 | Remapped | NC_000010.11 |
| NC_000011.10 | Chr11 | 75 | 204 | Remapped | NC_000011.10 |
| NC_000012.12 | Chr12 | 63 | 126 | Remapped | NC_000012.12 |
| NC_000013.11 | Chr13 | 46 | 67 | Remapped | NC_000013.11 |
| NC_000014.9 | Chr14 | 45 | 83 | Remapped | NC_000014.9 |
| NC_000015.10 | Chr15 | 42 | 119 | Remapped | NC_000015.10 |
| NC_000016.10 | Chr16 | 32 | 55 | Remapped | NC_000016.10 |
| NC_000017.11 | Chr17 | 27 | 61 | Remapped | NC_000017.11 |
| NC_000018.10 | Chr18 | 29 | 59 | Remapped | NC_000018.10 |
| NC_000019.10 | Chr19 | 61 | 159 | Remapped | NC_000019.10 |
| NC_000020.11 | Chr20 | 29 | 54 | Remapped | NC_000020.11 |
| NC_000021.9 | Chr21 | 23 | 47 | Remapped | NC_000021.9 |
| NC_000022.11 | Chr22 | 64 | 84 | Remapped | NC_000022.11 |
| NC_000023.11 | ChrX | 33 | 41 | Remapped | NC_000023.11 |
| NT_187515.1 | Chr1|NT_187515.1 | 1 | 2 | Remapped | NT_187515.1 |
| NT_187516.1 | Chr1|NT_187516.1 | 1 | 2 | Remapped | NT_187516.1 |
| NW_011332687.1 | Chr1|NW_011332687.1 | 1 | 2 | Remapped | NW_011332687.1 |
| NW_012132914.1 | Chr1|NW_012132914.1 | 4 | 12 | Remapped | NW_012132914.1 |
| NT_187523.1 | Chr2|NT_187523.1 | 1 | 2 | Remapped | NT_187523.1 |
| NT_187529.1 | Chr2|NT_187529.1 | 1 | 1 | Remapped | NT_187529.1 |
| NT_187647.1 | Chr2|NT_187647.1 | 1 | 2 | Remapped | NT_187647.1 |
| NW_011332689.1 | Chr2|NW_011332689.1 | 1 | 1 | Remapped | NW_011332689.1 |
| NW_019805488.1 | Chr3|NW_019805488.1 | 1 | 1 | Remapped | NW_019805488.1 |
| NW_019805489.1 | Chr3|NW_019805489.1 | 1 | 1 | Remapped | NW_019805489.1 |
| NT_187542.1 | Chr4|NT_187542.1 | 2 | 3 | Remapped | NT_187542.1 |
| NT_167246.2 | Chr6|NT_167246.2 | 6 | 16 | Remapped | NT_167246.2 |
| NT_167247.2 | Chr6|NT_167247.2 | 3 | 13 | Remapped | NT_167247.2 |
| NT_167248.2 | Chr6|NT_167248.2 | 6 | 16 | Remapped | NT_167248.2 |
| NT_167249.2 | Chr6|NT_167249.2 | 6 | 16 | Remapped | NT_167249.2 |
| NT_167245.2 | Chr6|NT_167245.2 | 1 | 1 | Remapped | NT_167245.2 |
| NT_113891.3 | Chr6|NT_113891.3 | 6 | 16 | Remapped | NT_113891.3 |
| NT_187555.1 | Chr6|NT_187555.1 | 1 | 1 | Remapped | NT_187555.1 |
| NW_009646200.1 | Chr6|NW_009646200.1 | 1 | 1 | Remapped | NW_009646200.1 |
| NW_018654713.1 | Chr6|NW_018654713.1 | 1 | 2 | Remapped | NW_018654713.1 |
| NT_187558.1 | Chr7|NT_187558.1 | 1 | 6 | Remapped | NT_187558.1 |
| NT_187562.1 | Chr7|NT_187562.1 | 7 | 32 | Remapped | NT_187562.1 |
| NT_187653.1 | Chr7|NT_187653.1 | 1 | 6 | Remapped | NT_187653.1 |
| NW_018654714.1 | Chr7|NW_018654714.1 | 2 | 3 | Remapped | NW_018654714.1 |
| NW_019805493.1 | Chr7|NW_019805493.1 | 1 | 2 | Remapped | NW_019805493.1 |
| NT_187576.1 | Chr8|NT_187576.1 | 2 | 2 | Remapped | NT_187576.1 |
| NT_187655.1 | Chr8|NT_187655.1 | 1 | 1 | Remapped | NT_187655.1 |
| NW_018654717.1 | Chr8|NW_018654717.1 | 6 | 9 | Remapped | NW_018654717.1 |
| NW_009646201.1 | Chr9|NW_009646201.1 | 1 | 1 | Remapped | NW_009646201.1 |
| NT_187583.1 | Chr11|NT_187583.1 | 1 | 1 | Remapped | NT_187583.1 |
| NW_011332695.1 | Chr11|NW_011332695.1 | 1 | 1 | Remapped | NW_011332695.1 |
| NW_019805497.1 | Chr11|NW_019805497.1 | 1 | 1 | Remapped | NW_019805497.1 |
| NT_187658.1 | Chr12|NT_187658.1 | 1 | 2 | Remapped | NT_187658.1 |
| NT_187587.1 | Chr12|NT_187587.1 | 4 | 7 | Remapped | NT_187587.1 |
| NT_187588.1 | Chr12|NT_187588.1 | 2 | 2 | Remapped | NT_187588.1 |
| NW_003315940.1 | Chr12|NW_003315940.1 | 1 | 2 | Remapped | NW_003315940.1 |
| NW_011332696.1 | Chr12|NW_011332696.1 | 3 | 6 | Remapped | NW_011332696.1 |
| NW_018654718.1 | Chr12|NW_018654718.1 | 1 | 5 | Remapped | NW_018654718.1 |
| NW_019805499.1 | Chr12|NW_019805499.1 | 1 | 1 | Remapped | NW_019805499.1 |
| NT_187600.1 | Chr14|NT_187600.1 | 6 | 14 | Remapped | NT_187600.1 |
| NT_187660.1 | Chr15|NT_187660.1 | 3 | 5 | Remapped | NT_187660.1 |
| NW_011332701.1 | Chr15|NW_011332701.1 | 3 | 5 | Remapped | NW_011332701.1 |
| NT_187607.1 | Chr16|NT_187607.1 | 1 | 1 | Remapped | NT_187607.1 |
| NW_012132921.1 | Chr16|NW_012132921.1 | 1 | 1 | Remapped | NW_012132921.1 |
| NW_017852933.1 | Chr16|NW_017852933.1 | 2 | 2 | Remapped | NW_017852933.1 |
| NT_187661.1 | Chr17|NT_187661.1 | 3 | 11 | Remapped | NT_187661.1 |
| NT_187663.1 | Chr17|NT_187663.1 | 2 | 5 | Remapped | NT_187663.1 |
| NT_187612.1 | Chr17|NT_187612.1 | 1 | 1 | Remapped | NT_187612.1 |
| NT_187614.1 | Chr17|NT_187614.1 | 3 | 11 | Remapped | NT_187614.1 |
| NW_003315953.2 | Chr17|NW_003315953.2 | 2 | 6 | Remapped | NW_003315953.2 |
| NW_014040928.1 | Chr18|NW_014040928.1 | 1 | 2 | Remapped | NW_014040928.1 |
| NT_187693.1 | Chr19|NT_187693.1 | 7 | 55 | Remapped | NT_187693.1 |
| NW_003571061.2 | Chr19|NW_003571061.2 | 3 | 3 | Remapped | NW_003571061.2 |
| NW_003571057.2 | Chr19|NW_003571057.2 | 1 | 1 | Remapped | NW_003571057.2 |
| NW_003571058.2 | Chr19|NW_003571058.2 | 1 | 1 | Remapped | NW_003571058.2 |
| NW_003571059.2 | Chr19|NW_003571059.2 | 1 | 1 | Remapped | NW_003571059.2 |
| NW_003571060.1 | Chr19|NW_003571060.1 | 6 | 39 | Remapped | NW_003571060.1 |
| NW_003571056.2 | Chr19|NW_003571056.2 | 1 | 1 | Remapped | NW_003571056.2 |
| NW_003571055.2 | Chr19|NW_003571055.2 | 1 | 1 | Remapped | NW_003571055.2 |
| NT_187620.1 | Chr19|NT_187620.1 | 1 | 2 | Remapped | NT_187620.1 |
| NW_003315962.1 | Chr19|NW_003315962.1 | 1 | 1 | Remapped | NW_003315962.1 |
| NW_003315965.1 | Chr19|NW_003315965.1 | 1 | 1 | Remapped | NW_003315965.1 |
| NW_003571054.1 | Chr19|NW_003571054.1 | 6 | 39 | Remapped | NW_003571054.1 |
| NW_014040929.1 | Chr19|NW_014040929.1 | 1 | 1 | Remapped | NW_014040929.1 |
| NW_003315968.2 | Chr21|NW_003315968.2 | 1 | 12 | Remapped | NW_003315968.2 |
| NT_187629.1 | Chr22|NT_187629.1 | 13 | 13 | Remapped | NT_187629.1 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.10 | Chr1 | 90 | 218 | Remapped | NC_000001.10 |
| NC_000002.11 | Chr2 | 117 | 275 | Remapped | NC_000002.11 |
| NC_000003.11 | Chr3 | 77 | 175 | Remapped | NC_000003.11 |
| NC_000004.11 | Chr4 | 91 | 221 | Remapped | NC_000004.11 |
| NC_000005.9 | Chr5 | 80 | 172 | Remapped | NC_000005.9 |
| NC_000006.11 | Chr6 | 68 | 159 | Remapped | NC_000006.11 |
| NC_000007.13 | Chr7 | 90 | 162 | Remapped | NC_000007.13 |
| NC_000008.10 | Chr8 | 85 | 215 | Remapped | NC_000008.10 |
| NC_000009.11 | Chr9 | 66 | 90 | Remapped | NC_000009.11 |
| NC_000010.10 | Chr10 | 48 | 124 | Remapped | NC_000010.10 |
| NC_000011.9 | Chr11 | 75 | 204 | Remapped | NC_000011.9 |
| NC_000012.11 | Chr12 | 63 | 126 | Remapped | NC_000012.11 |
| NC_000013.10 | Chr13 | 46 | 67 | Remapped | NC_000013.10 |
| NC_000014.8 | Chr14 | 45 | 83 | Remapped | NC_000014.8 |
| NC_000015.9 | Chr15 | 42 | 119 | Remapped | NC_000015.9 |
| NC_000016.9 | Chr16 | 32 | 55 | Remapped | NC_000016.9 |
| NC_000017.10 | Chr17 | 27 | 61 | Remapped | NC_000017.10 |
| NC_000018.9 | Chr18 | 29 | 59 | Remapped | NC_000018.9 |
| NC_000019.9 | Chr19 | 60 | 158 | Remapped | NC_000019.9 |
| NC_000020.10 | Chr20 | 29 | 54 | Remapped | NC_000020.10 |
| NC_000021.8 | Chr21 | 23 | 47 | Remapped | NC_000021.8 |
| NC_000022.10 | Chr22 | 64 | 84 | Remapped | NC_000022.10 |
| NC_000023.10 | ChrX | 33 | 41 | Remapped | NC_000023.10 |
| NW_003871055.3 | Chr1|NW_003871055.3 | 5 | 31 | Remapped | NW_003871055.3 |
| NW_003871058.1 | Chr3|NW_003871058.1 | 1 | 2 | Remapped | NW_003871058.1 |
| NW_004775427.1 | Chr4|NW_004775427.1 | 1 | 3 | Remapped | NW_004775427.1 |
| NW_004775428.1 | Chr5|NW_004775428.1 | 1 | 1 | Remapped | NW_004775428.1 |
| NT_113891.2 | Chr6|NT_113891.2 | 6 | 16 | Remapped | NT_113891.2 |
| NT_167245.1 | Chr6|NT_167245.1 | 1 | 1 | Remapped | NT_167245.1 |
| NT_167246.1 | Chr6|NT_167246.1 | 6 | 16 | Remapped | NT_167246.1 |
| NT_167247.1 | Chr6|NT_167247.1 | 3 | 13 | Remapped | NT_167247.1 |
| NT_167248.1 | Chr6|NT_167248.1 | 6 | 16 | Remapped | NT_167248.1 |
| NT_167249.1 | Chr6|NT_167249.1 | 6 | 16 | Remapped | NT_167249.1 |
| NW_003571040.1 | Chr7|NW_003571040.1 | 7 | 32 | Remapped | NW_003571040.1 |
| NW_003871064.1 | Chr7|NW_003871064.1 | 3 | 7 | Remapped | NW_003871064.1 |
| NW_003315923.1 | Chr8|NW_003315923.1 | 1 | 1 | Remapped | NW_003315923.1 |
| NW_003571042.1 | Chr8|NW_003571042.1 | 2 | 2 | Remapped | NW_003571042.1 |
| NW_003315925.1 | Chr9|NW_003315925.1 | 1 | 1 | Remapped | NW_003315925.1 |
| NW_003871068.1 | Chr10|NW_003871068.1 | 3 | 11 | Remapped | NW_003871068.1 |
| NW_003571045.1 | Chr11|NW_003571045.1 | 1 | 2 | Remapped | NW_003571045.1 |
| NW_004070871.1 | Chr11|NW_004070871.1 | 1 | 1 | Remapped | NW_004070871.1 |
| NW_003315940.1 | Chr12|NW_003315940.1 | 1 | 2 | Remapped | NW_003315940.1 |
| NW_004166863.1 | Chr14|NW_004166863.1 | 13 | 29 | Remapped | NW_004166863.1 |
| NW_003871085.1 | Chr16|NW_003871085.1 | 1 | 1 | Remapped | NW_003871085.1 |
| NW_003315949.1 | Chr17|NW_003315949.1 | 3 | 11 | Remapped | NW_003315949.1 |
| NW_003315950.2 | Chr17|NW_003315950.2 | 1 | 1 | Remapped | NW_003315950.2 |
| NW_003315953.1 | Chr17|NW_003315953.1 | 3 | 7 | Remapped | NW_003315953.1 |
| NW_003871086.1 | Chr17|NW_003871086.1 | 3 | 18 | Remapped | NW_003871086.1 |
| NW_003315962.1 | Chr19|NW_003315962.1 | 1 | 1 | Remapped | NW_003315962.1 |
| NW_003315965.1 | Chr19|NW_003315965.1 | 1 | 1 | Remapped | NW_003315965.1 |
| NW_003571053.2 | Chr19|NW_003571053.2 | 4 | 21 | Remapped | NW_003571053.2 |
| NW_004166865.1 | Chr19|NW_004166865.1 | 2 | 17 | Remapped | NW_004166865.1 |
| NW_004775434.1 | Chr19|NW_004775434.1 | 1 | 2 | Remapped | NW_004775434.1 |
| NW_003315968.1 | Chr21|NW_003315968.1 | 1 | 12 | Remapped | NW_003315968.1 |
| NW_003871096.1 | Chr22|NW_003871096.1 | 1 | 1 | Remapped | NW_003871096.1 |
| NW_003871103.3 | ChrX|NW_003871103.3 | 1 | 1 | Remapped | NW_003871103.3 |
| NW_004070880.2 | ChrX|NW_004070880.2 | 1 | 4 | Remapped | NW_004070880.2 |
| NW_004070887.1 | ChrX|NW_004070887.1 | 1 | 1 | Remapped | NW_004070887.1 |
| NW_004070888.1 | ChrX|NW_004070888.1 | 1 | 1 | Remapped | NW_004070888.1 |
| NW_004070890.2 | ChrX|NW_004070890.2 | 2 | 3 | Remapped | NW_004070890.2 |
| NW_004166866.1 | ChrX|NW_004166866.1 | 1 | 1 | Remapped | NW_004166866.1 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.8 | Chr1 | 90 | 218 | Submitted | NC_000001.8 |
| NC_000002.9 | Chr2 | 117 | 275 | Submitted | NC_000002.9 |
| NC_000003.9 | Chr3 | 77 | 175 | Submitted | NC_000003.9 |
| NC_000004.9 | Chr4 | 91 | 221 | Submitted | NC_000004.9 |
| NC_000005.8 | Chr5 | 80 | 172 | Submitted | NC_000005.8 |
| NC_000006.9 | Chr6 | 68 | 159 | Submitted | NC_000006.9 |
| NC_000007.11 | Chr7 | 91 | 163 | Submitted | NC_000007.11 |
| NC_000008.9 | Chr8 | 85 | 215 | Submitted | NC_000008.9 |
| NC_000009.9 | Chr9 | 66 | 90 | Submitted | NC_000009.9 |
| NC_000010.8 | Chr10 | 48 | 124 | Submitted | NC_000010.8 |
| NC_000011.8 | Chr11 | 75 | 204 | Submitted | NC_000011.8 |
| NC_000012.9 | Chr12 | 63 | 126 | Submitted | NC_000012.9 |
| NC_000013.9 | Chr13 | 46 | 67 | Submitted | NC_000013.9 |
| NC_000014.7 | Chr14 | 45 | 83 | Submitted | NC_000014.7 |
| NC_000015.8 | Chr15 | 42 | 119 | Submitted | NC_000015.8 |
| NC_000016.8 | Chr16 | 32 | 55 | Submitted | NC_000016.8 |
| NC_000017.9 | Chr17 | 27 | 61 | Submitted | NC_000017.9 |
| NC_000018.8 | Chr18 | 29 | 59 | Submitted | NC_000018.8 |
| NC_000019.8 | Chr19 | 62 | 175 | Submitted | NC_000019.8 |
| NC_000020.9 | Chr20 | 29 | 54 | Submitted | NC_000020.9 |
| NC_000021.7 | Chr21 | 23 | 47 | Submitted | NC_000021.7 |
| NC_000022.8 | Chr22 | 64 | 84 | Submitted | NC_000022.8 |
| NC_000023.8 | ChrX | 33 | 41 | Submitted | NC_000023.8 |
| Variant Region remap status | Variant Call remap status | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sequence ID | Chr | Variant Regions on source | Perfect | Good | Pass | Fail | Mult | Variant Calls on source | Perfect | Good | Pass | Fail | Mult |
| NC_000001.8 | Chr1 | 90 | 82 | 0 | 3 | 0 | 5 | 218 | 183 | 0 | 4 | 0 | 31 |
| NC_000002.9 | Chr2 | 117 | 113 | 0 | 4 | 0 | 0 | 275 | 267 | 0 | 8 | 0 | 0 |
| NC_000003.9 | Chr3 | 77 | 76 | 0 | 0 | 0 | 1 | 175 | 173 | 0 | 0 | 0 | 2 |
| NC_000004.9 | Chr4 | 91 | 90 | 0 | 0 | 0 | 1 | 221 | 218 | 0 | 0 | 0 | 3 |
| NC_000005.8 | Chr5 | 80 | 76 | 3 | 0 | 0 | 1 | 172 | 163 | 8 | 0 | 0 | 1 |
| NC_000006.9 | Chr6 | 68 | 62 | 0 | 0 | 0 | 6 | 159 | 143 | 0 | 0 | 0 | 16 |
| NC_000007.11 | Chr7 | 91 | 80 | 2 | 0 | 0 | 9 | 163 | 123 | 2 | 0 | 0 | 38 |
| NC_000008.9 | Chr8 | 85 | 81 | 1 | 0 | 0 | 3 | 215 | 211 | 1 | 0 | 0 | 3 |
| NC_000009.9 | Chr9 | 66 | 65 | 0 | 0 | 0 | 1 | 90 | 89 | 0 | 0 | 0 | 1 |
| NC_000010.8 | Chr10 | 48 | 45 | 0 | 0 | 0 | 3 | 124 | 113 | 0 | 0 | 0 | 11 |
| NC_000011.8 | Chr11 | 75 | 73 | 0 | 0 | 0 | 2 | 204 | 201 | 0 | 0 | 0 | 3 |
| NC_000012.9 | Chr12 | 63 | 62 | 0 | 0 | 0 | 1 | 126 | 124 | 0 | 0 | 0 | 2 |
| NC_000013.9 | Chr13 | 46 | 46 | 0 | 0 | 0 | 0 | 67 | 67 | 0 | 0 | 0 | 0 |
| NC_000014.7 | Chr14 | 45 | 30 | 1 | 1 | 0 | 13 | 83 | 52 | 1 | 1 | 0 | 29 |
| NC_000015.8 | Chr15 | 42 | 40 | 1 | 1 | 0 | 0 | 119 | 117 | 1 | 1 | 0 | 0 |
| NC_000016.8 | Chr16 | 32 | 31 | 0 | 0 | 0 | 1 | 55 | 54 | 0 | 0 | 0 | 1 |
| NC_000017.9 | Chr17 | 27 | 15 | 1 | 1 | 0 | 10 | 61 | 21 | 1 | 2 | 0 | 37 |
| NC_000018.8 | Chr18 | 29 | 29 | 0 | 0 | 0 | 0 | 59 | 59 | 0 | 0 | 0 | 0 |
| NC_000019.8 | Chr19 | 62 | 52 | 1 | 2 | 0 | 7 | 175 | 132 | 16 | 2 | 0 | 25 |
| NC_000020.9 | Chr20 | 29 | 29 | 0 | 0 | 0 | 0 | 54 | 54 | 0 | 0 | 0 | 0 |
| NC_000021.7 | Chr21 | 23 | 22 | 0 | 0 | 0 | 1 | 47 | 35 | 0 | 0 | 0 | 12 |
| NC_000022.8 | Chr22 | 64 | 63 | 0 | 0 | 0 | 1 | 84 | 83 | 0 | 0 | 0 | 1 |
| NC_000023.8 | ChrX | 33 | 26 | 0 | 0 | 0 | 7 | 41 | 30 | 0 | 0 | 0 | 11 |
| Variant Region remap status | Variant Call remap status | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sequence ID | Chr | Variant Regions on source | Perfect | Good | Pass | Fail | Mult | Variant Calls on source | Perfect | Good | Pass | Fail | Mult |
| NC_000001.8 | Chr1 | 90 | 75 | 6 | 2 | 0 | 7 | 218 | 166 | 32 | 2 | 0 | 18 |
| NC_000002.9 | Chr2 | 117 | 108 | 4 | 2 | 0 | 3 | 275 | 251 | 16 | 4 | 0 | 4 |
| NC_000003.9 | Chr3 | 77 | 73 | 2 | 0 | 0 | 2 | 175 | 170 | 3 | 0 | 0 | 2 |
| NC_000004.9 | Chr4 | 91 | 86 | 3 | 0 | 0 | 2 | 221 | 213 | 5 | 0 | 0 | 3 |
| NC_000005.8 | Chr5 | 80 | 76 | 4 | 0 | 0 | 0 | 172 | 161 | 11 | 0 | 0 | 0 |
| NC_000006.9 | Chr6 | 68 | 57 | 2 | 0 | 0 | 9 | 159 | 137 | 2 | 0 | 0 | 20 |
| NC_000007.11 | Chr7 | 91 | 74 | 7 | 0 | 0 | 10 | 163 | 114 | 10 | 0 | 0 | 39 |
| NC_000008.9 | Chr8 | 85 | 75 | 1 | 0 | 0 | 9 | 215 | 202 | 1 | 0 | 0 | 12 |
| NC_000009.9 | Chr9 | 66 | 64 | 1 | 0 | 0 | 1 | 90 | 88 | 1 | 0 | 0 | 1 |
| NC_000010.8 | Chr10 | 48 | 47 | 0 | 1 | 0 | 0 | 124 | 123 | 0 | 1 | 0 | 0 |
| NC_000011.8 | Chr11 | 75 | 72 | 1 | 0 | 0 | 2 | 204 | 196 | 6 | 0 | 0 | 2 |
| NC_000012.9 | Chr12 | 63 | 50 | 0 | 0 | 0 | 13 | 126 | 101 | 0 | 0 | 0 | 25 |
| NC_000013.9 | Chr13 | 46 | 46 | 0 | 0 | 0 | 0 | 67 | 67 | 0 | 0 | 0 | 0 |
| NC_000014.7 | Chr14 | 45 | 26 | 12 | 1 | 0 | 6 | 83 | 44 | 24 | 1 | 0 | 14 |
| NC_000015.8 | Chr15 | 42 | 38 | 0 | 1 | 0 | 3 | 119 | 113 | 0 | 1 | 0 | 5 |
| NC_000016.8 | Chr16 | 32 | 27 | 1 | 0 | 0 | 4 | 55 | 50 | 1 | 0 | 0 | 4 |
| NC_000017.9 | Chr17 | 27 | 14 | 5 | 0 | 0 | 8 | 61 | 20 | 18 | 0 | 0 | 23 |
| NC_000018.8 | Chr18 | 29 | 28 | 0 | 0 | 0 | 1 | 59 | 57 | 0 | 0 | 0 | 2 |
| NC_000019.8 | Chr19 | 62 | 49 | 3 | 0 | 0 | 10 | 175 | 128 | 3 | 0 | 0 | 44 |
| NC_000020.9 | Chr20 | 29 | 28 | 1 | 0 | 0 | 0 | 54 | 53 | 1 | 0 | 0 | 0 |
| NC_000021.7 | Chr21 | 23 | 22 | 0 | 0 | 0 | 1 | 47 | 35 | 0 | 0 | 0 | 12 |
| NC_000022.8 | Chr22 | 64 | 27 | 24 | 0 | 0 | 13 | 84 | 36 | 35 | 0 | 0 | 13 |
| NC_000023.8 | ChrX | 33 | 29 | 4 | 0 | 0 | 0 | 41 | 33 | 8 | 0 | 0 | 0 |
Samplesets
Number of Samplesets: 1
- Sampleset Type:
- Control
- Description:
- 16 CEU father-mother-offspring trios from Utah [CEU], 12 Yoruba trios from Ibadan, Nigeria [YRI], 28 unrelated Chinese and Japanese individuals from Beijing and Tokyo, respectively [CHB+JPT].
- Size:
- 112
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- None reported
| Sample ID | Cell Type | Subject ID | Sex | Ethnicity | Subject Age | Subject Phenotype |
|---|---|---|---|---|---|---|
| NA12812 | B-Lymphocyte | NA12812 | Male | CEU | Not reported | |
| NA07348 | B-Lymphocyte | NA07348 | Female | CEU | 45 Years | Not reported |
| NA11993 | B-Lymphocyte | NA11993 | Female | CEU | 80 Years | Not reported |
| NA18577 | B-Lymphocyte | NA18577 | Female | CHB | Not reported | |
| NA18558 | B-Lymphocyte | NA18558 | Male | CHB | Not reported | |
| NA12813 | B-Lymphocyte | NA12813 | Female | CEU | Not reported | |
| NA19145 | B-Lymphocyte | NA19145 | Male | YRI | Not reported | |
| NA19142 | B-Lymphocyte | NA19142 | Male | YRI | Not reported | |
| NA18608 | B-Lymphocyte | NA18608 | Male | CHB | Not reported | |
| NA12154 | B-Lymphocyte | NA12154 | Male | CEU | 92 Years | Not reported |
| NA12057 | B-Lymphocyte | NA12057 | Female | CEU | 75 Years | Not reported |
| NA19137 | B-Lymphocyte | NA19137 | Female | YRI | Not reported | |
| NA19094 | B-Lymphocyte | NA19094 | Female | YRI | Not reported | |
| NA10857 | B-Lymphocyte | NA10857 | Male | CEU | 47 Years | Not reported |
| NA18852 | B-Lymphocyte | NA18852 | Female | YRI | Not reported | |
| NA11881 | B-Lymphocyte | NA11881 | Male | CEU | 62 Years | Not reported |
| NA19116 | B-Lymphocyte | NA19116 | Female | YRI | Not reported | |
| NA18609 | B-Lymphocyte | NA18609 | Male | CHB | Not reported | |
| NA06993 | B-Lymphocyte | NA06993 | Male | CEU | 74 Years | Not reported |
| NA10830 | B-Lymphocyte | NA10830 | Male | CEU | 66 Years | Not reported |
| NA19138 | B-Lymphocyte | NA19138 | Male | YRI | Not reported | |
| NA18960 | B-Lymphocyte | NA18960 | Male | JPT | Not reported | |
| NA12056 | B-Lymphocyte | NA12056 | Male | CEU | 79 Years | Not reported |
| NA19092 | B-Lymphocyte | NA19092 | Male | YRI | Not reported | |
| NA12236 | B-Lymphocyte | NA12236 | Female | CEU | 86 Years | Not reported |
| NA19119 | B-Lymphocyte | NA19119 | Male | YRI | Not reported | |
| NA12751 | B-Lymphocyte | NA12751 | Female | CEU | Not reported | |
| NA19003 | B-Lymphocyte | NA19003 | Female | JPT | Not reported | |
| NA18952 | B-Lymphocyte | NA18952 | Male | JPT | Not reported | |
| NA12146 | B-Lymphocyte | NA12146 | Male | CEU | 61 Years | Not reported |
| NA18537 | B-Lymphocyte | NA18537 | Female | CHB | Not reported | |
| NA18855 | B-Lymphocyte | NA18855 | Female | YRI | Not reported | |
| NA18854 | B-Lymphocyte | NA18854 | Male | YRI | Not reported | |
| NA12865 | B-Lymphocyte | NA12865 | Female | CEU | Not reported | |
| NA12249 | B-Lymphocyte | NA12249 | Female | CEU | 77 Years | Not reported |
| NA12892 | B-Lymphocyte | NA12892 | Female | CEU | Not reported | |
| NA10859 | B-Lymphocyte | NA10859 | Female | CEU | 41 Years | Not reported |
| NA18949 | B-Lymphocyte | NA18949 | Female | JPT | Not reported | |
| NA06991 | B-Lymphocyte | NA06991 | Female | CEU | 42 Years | Not reported |
| NA18992 | B-Lymphocyte | NA18992 | Female | JPT | Not reported | |
| NA18856 | B-Lymphocyte | NA18856 | Male | YRI | Not reported | |
| NA11995 | B-Lymphocyte | NA11995 | Female | CEU | 84 Years | Not reported |
| NA18853 | B-Lymphocyte | NA18853 | Male | YRI | Not reported | |
| NA18612 | B-Lymphocyte | NA18612 | Male | CHB | Not reported | |
| NA18951 | B-Lymphocyte | NA18951 | Female | JPT | Not reported | |
| NA19144 | B-Lymphocyte | NA19144 | Male | YRI | Not reported | |
| NA11992 | B-Lymphocyte | NA11992 | Male | CEU | 86 Years | Not reported |
| NA18857 | B-Lymphocyte | NA18857 | Male | YRI | Not reported | |
| NA12043 | B-Lymphocyte | NA12043 | Male | CEU | 74 Years | Not reported |
| NA18542 | B-Lymphocyte | NA18542 | Female | CHB | Not reported | |
| NA10860 | B-Lymphocyte | NA10860 | Male | CEU | 50 Years | Not reported |
| NA06985 | B-Lymphocyte | NA06985 | Female | CEU | 69 Years | Not reported |
| NA18593 | B-Lymphocyte | NA18593 | Female | CHB | Not reported | |
| NA12044 | B-Lymphocyte | NA12044 | Female | CEU | 70 Years | Not reported |
| NA12234 | B-Lymphocyte | NA12234 | Female | CEU | 74 Years | Not reported |
| NA12264 | B-Lymphocyte | NA12264 | Male | CEU | 72 Years | Not reported |
| NA19143 | B-Lymphocyte | NA19143 | Female | YRI | Not reported | |
| NA19141 | B-Lymphocyte | NA19141 | Male | YRI | Not reported | |
| NA10851 | B-Lymphocyte | NA10851 | Male | CEU | 52 Years | Not reported |
| NA12874 | B-Lymphocyte | NA12874 | Male | CEU | Not reported | |
| NA19140 | B-Lymphocyte | NA19140 | Female | YRI | Not reported | |
| NA07029 | B-Lymphocyte | NA07029 | Male | CEU | 47 Years | Not reported |
| NA07357 | B-Lymphocyte | NA07357 | Male | CEU | 69 Years | Not reported |
| NA18965 | B-Lymphocyte | NA18965 | Male | JPT | Not reported | |
| NA06994 | B-Lymphocyte | NA06994 | Male | CEU | 68 Years | Not reported |
| NA18550 | B-Lymphocyte | NA18550 | Female | CHB | Not reported | |
| NA18987 | B-Lymphocyte | NA18987 | Female | JPT | Not reported | |
| NA18953 | B-Lymphocyte | NA18953 | Male | JPT | Not reported | |
| NA18529 | B-Lymphocyte | NA18529 | Female | CHB | Not reported | |
| NA12878 | B-Lymphocyte | NA12878 | Female | CEU | Not reported | |
| NA18971 | B-Lymphocyte | NA18971 | Male | JPT | Not reported | |
| NA18999 | B-Lymphocyte | NA18999 | Female | JPT | Not reported | |
| NA11994 | B-Lymphocyte | NA11994 | Male | CEU | 80 Years | Not reported |
| NA12248 | B-Lymphocyte | NA12248 | Male | CEU | 89 Years | Not reported |
| NA07345 | B-Lymphocyte | NA07345 | Female | CEU | 69 Years | Not reported |
| NA10847 | B-Lymphocyte | NA10847 | Female | CEU | 38 Years | Not reported |
| NA19120 | B-Lymphocyte | NA19120 | Male | YRI | Not reported | |
| NA19093 | B-Lymphocyte | NA19093 | Female | YRI | Not reported | |
| NA18994 | B-Lymphocyte | NA18994 | Male | JPT | Not reported | |
| NA12891 | B-Lymphocyte | NA12891 | Male | CEU | Not reported | |
| NA18944 | B-Lymphocyte | NA18944 | Male | JPT | Not reported | |
| NA12801 | B-Lymphocyte | NA12801 | Male | CEU | Not reported | |
| NA10863 | B-Lymphocyte | NA10863 | Female | CEU | 43 Years | Not reported |
| NA18516 | B-Lymphocyte | NA18516 | Male | YRI | Not reported | |
| NA11882 | B-Lymphocyte | NA11882 | Female | CEU | 61 Years | Not reported |
| NA18547 | B-Lymphocyte | NA18547 | Female | CHB | Not reported | |
| NA18972 | B-Lymphocyte | NA18972 | Female | JPT | Not reported | |
| NA10835 | B-Lymphocyte | NA10835 | Male | CEU | 39 Years | Not reported |
| NA18576 | B-Lymphocyte | NA18576 | Female | CHB | Not reported | |
| NA19139 | B-Lymphocyte | NA19139 | Male | YRI | Not reported | |
| NA18978 | B-Lymphocyte | NA18978 | Female | JPT | Not reported | |
| NA10861 | B-Lymphocyte | NA10861 | Female | CEU | 49 Years | Not reported |
| NA12875 | B-Lymphocyte | NA12875 | Female | CEU | Not reported | |
| NA12750 | B-Lymphocyte | NA12750 | Male | CEU | Not reported | |
| NA07000 | B-Lymphocyte | NA07000 | Female | CEU | 66 Years | Not reported |
| NA12740 | B-Lymphocyte | NA12740 | Female | CEU | Not reported | |
| NA18517 | B-Lymphocyte | NA18517 | Female | YRI | Not reported | |
| NA12239 | B-Lymphocyte | NA12239 | Female | CEU | 61 Years | Not reported |
| NA18968 | B-Lymphocyte | NA18968 | Female | JPT | Not reported | |
| NA18515 | B-Lymphocyte | NA18515 | Male | YRI | Not reported |
Experimental Details
| Experiment ID | Type | Method | Analysis | Platforms | Number of Variant Calls |
|---|---|---|---|---|---|
| 1 | Discovery | SNP array | Probe signal intensity | GPL6433 | 2,987 |